[gentoo-commits] repo/gentoo:master commit in: sci-libs/libmems/files/, sci-libs/libmems/

[Justin Lecher]

commit:     319e280a8e026786b319d48de907e440049f490c
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Thu Dec 24 23:32:17 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 25 11:44:51 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=319e280a

sci-libs/libmems: Version bump, fix bug 529770 and QA issues.

Package-Manager: portage-2.2.26

 .../files/libmems-1.6_p1-broken-constness.patch    | 24 +++++++++++++++
 sci-libs/libmems/files/libmems-1.6_p1-build.patch  | 10 ++++++
 sci-libs/libmems/libmems-1.6_p1-r1.ebuild          | 36 ++++++++++++++++++++++
 3 files changed, 70 insertions(+)

diff --git a/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch
new file mode 100644
index 0000000..0bd922c
--- /dev/null
+++ b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch
@@ -0,0 +1,24 @@
+Fix bug 529770 caused by non-const copy constructor.
+
+--- libmems-1.6_p1/libMems/Aligner.cpp
++++ libmems-1.6_p1/libMems/Aligner.cpp
+@@ -939,7 +939,7 @@
+ 	MatchLeftEndComparator( unsigned seq = 0 ){
+ 		m_seq = seq;
+ 	}
+-	MatchLeftEndComparator( MatchLeftEndComparator& msc ){
++	MatchLeftEndComparator( const MatchLeftEndComparator& msc ){
+ 		m_seq = msc.m_seq;
+ 	}
+ 	// TODO??  make this do a wraparound comparison if all is equal?
+--- libmems-1.6_p1/libMems/Aligner.h
++++ libmems-1.6_p1/libMems/Aligner.h
+@@ -49,7 +49,7 @@
+ 	LabeledMemComparator( uint seq ){
+ 		m_seq = seq;
+ 	}
+-	LabeledMemComparator( LabeledMemComparator& lmc ){
++	LabeledMemComparator( const LabeledMemComparator& lmc ){
+ 		m_seq = lmc.m_seq;
+ 	}
+ 	boolean operator()(const LabeledMem& a, const LabeledMem& b) const{

diff --git a/sci-libs/libmems/files/libmems-1.6_p1-build.patch b/sci-libs/libmems/files/libmems-1.6_p1-build.patch
index 63e5f12..04d5dd9 100644
--- a/sci-libs/libmems/files/libmems-1.6_p1-build.patch
+++ b/sci-libs/libmems/files/libmems-1.6_p1-build.patch
@@ -17,3 +17,13 @@ index 6101f71..d66053d 100644
  
  LIBMEMS_H = \
  RepeatHash.h      MatchHashEntry.h \
+--- a/libMems/dmSML/util.c
++++ b/libMems/dmSML/util.c
+@@ -2,6 +2,7 @@
+ #include "config.h"
+ #endif
+ 
++#include <stdlib.h>
+ #include <stdio.h>
+ #include "libMems/dmSML/util.h"
+ 

diff --git a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
new file mode 100644
index 0000000..2e094ab
--- /dev/null
+++ b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Library for sci-biology/mauve"
+HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE="doc"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="
+	dev-libs/boost
+	sci-libs/libgenome
+	sci-libs/libmuscle"
+DEPEND="${CDEPEND}
+	doc? ( app-doc/doxygen )"
+RDEPEND="${CDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-build.patch
+	"${FILESDIR}"/${P}-boost.patch
+	"${FILESDIR}"/${P}-gcc-4.7.patch
+	"${FILESDIR}"/${P}-broken-constness.patch
+	)
+
+src_prepare() {
+	default
+	eautoreconf
+}